I am a new Gromacs user . I want to do simulation of laccase with its ligand (N-acetyl-D-golocosamin)(NAG) which is a suger whith gromose 54a7 and I use the ATB server for production of ligand topology .I neutralized my system whith this command line
gmx genion -s ions.tpr -o ions.gro -p topol.top -pname NA -nname CL -neutral
but when I typed this command line
gmx grompp -f minim.mdp -c ions.gro -p topol.top -o em.tpr
I saw this Note: " System has non-zero total charge: -0.000368 .Total charge should normally be an integer" and also a warning: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration.
Is it possile the decimal charge be related to charges in .itp file from ATB? If so how I can resolve this issue?
Seems like you have the decimal charge form the ATB. Your total charge should be an integer when you get it from ATB then you can add the counter ion to make it zero.
If ATB charge is not exactly zero, you can tweak it a little bit in your itp to make it zero-based on your understanding of the chemical structure, especially in a case like where your difference is very small ( -0.000368).
Two questions and thus two answers.
The first one is non-integer charge. This is caused in parametrization of your system. As the net charge is quite small, you can ignore it and run the simulation. If it is large, you need to reparametrize it, which obviously is not the case here.
The second one is the concentration of ions. This can be done When you neutralize your system. Just add a -conc flag is fine.
Hi Azam,
The net charge that remains after neutralization is quite small to be a problem. Additionally, to replicate physiology concentration (100 mM), you should add -conc 0.1 in your genion command line.
Thanks every one for your answers. I used the -conc flag for neutralize my system and again the total charge of system was - 000.368, so I decided to ignore it. can you tell me whats the command- line to use the -maxwarn option.
Azam Roohi Mam! Can you take in the initial molecule and energy minimize with some other software like swiss PBD viewer and redo the procedure? This can rectify your error. Sometimes failing to fix the missing chains might also create this issue
Hi Thirumal Kumar,
thanks for your recommendation.I resolved that issue in another way.
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